Test Report

Environment

Packages

{'pytest': '3.7.1', 'py': '1.5.4', 'pluggy': '0.7.1'}

Platform

Linux-3.10.0-514.21.1.el7.x86_64-x86_64-with-redhat-7.3-Maipo

Plugins

{'xdist': '1.22.5', 'timeout': '1.3.1', 'metadata': '1.7.0', 'html': '1.19.0', 'forked': '0.2'}

Python

3.6.3

Results

Result	Test	Duration
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-distance 500 --overwrite]	0.14
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939fa67a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 83.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --overwrite]	0.12
[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fd4433119e8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 87.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-info H2 --overwrite]	0.14
[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f41a5866d68>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.1 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-max 0.3 --overwrite]	0.22
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8d84c88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 88.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-flag s50 --overwrite]	0.16
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9f1588>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 224.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-include-info DB --overwrite]	0.16
[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fd443332518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 8.0 kB CPU Usage: 99.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-max 12 --overwrite]	0.21
[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f0308c4aa20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1200.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]	0.23
[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f4f0e1b59e8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1968.0 kB CPU Usage: 99.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-distance 500 --overwrite]	0.22
[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f7f012dba20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 99.3 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]	0.21
[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fef3b955f60>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 87.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-info DB --overwrite]	0.20
[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f5596f71c88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 3624.0 kB CPU Usage: 99.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]	0.20
[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1fa098ab38>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 204.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-min 0.2 --overwrite]	0.21
[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe3442549e8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 89.4 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]	0.21
[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc9f8dd7a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 8.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]	0.22
[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f976b750f60>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 764.0 kB CPU Usage: 99.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]	0.20
[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f58fced9a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 140.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]	0.20
[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa34e0eda20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 960.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --overwrite]	0.24
[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7ff8bbfbcc88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 8.0 kB CPU Usage: 99.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-min 8 --overwrite]	0.20
[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fcebf611a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 99.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]	0.13
[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fbb1fe8ca20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]	0.20
[gw34] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1bf07a8a90>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 88.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]	0.19
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8dae4e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]	0.27
[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f41a589a518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --overwrite]	0.12
[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f0308c6b550>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 89.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-mac-min 8 --overwrite]	0.15
[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fef393ed4e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]	0.13
[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f5596f9f4e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 89.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]	0.13
[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe3441d6518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 89.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]	0.13
[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7ff8bbfee4e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]	0.22
[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f8a9199ca20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]	0.13
[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f91da1fca58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-flag s50 --overwrite]	0.13
[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f0c290499e8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1208.0 kB CPU Usage: 89.1 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-maf-min 0.2 --overwrite]	0.14
[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f58fce9d588>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 89.3 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]	0.14
[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9b5a0fdd8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]	0.14
[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f976b77f588>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 97.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --overwrite]	0.13
[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f27c36a5a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]	0.14
[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa05687aa90>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --overwrite]	0.15
[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62f98f69b0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 89.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]	0.16
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc76ba20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 99.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]	0.25
[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa6d1b1d9b0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 99.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-info H2 --overwrite]	0.18
[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f4f0e1d6518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1200.0 kB CPU Usage: 99.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]	0.14
[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f26cbd87b70>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --overwrite]	0.13
[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1fa09a1630>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]	0.18
[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe532e85a20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]	0.15
[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fcebf630588>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 88.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]	0.17
[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f948e46fd68>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 86.1 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]	0.18
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36b1cdfa20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1200.0 kB CPU Usage: 89.2 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]	0.18
[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fd7dce9ca58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1200.0 kB CPU Usage: 99.1 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]	0.18
[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f7274d53a20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 204.0 kB CPU Usage: 94.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]	0.18
[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fdc758c1390>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 144.0 kB CPU Usage: 98.1 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --overwrite]	0.19
[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc976ffea58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 8.0 kB CPU Usage: 89.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]	0.18
[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1773e509e8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 764.0 kB CPU Usage: 99.1 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]	0.18
[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7ff99e9125f8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 89.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]	0.19
[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f6ec4aff550>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 89.2 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --overwrite]	0.19
[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa49ab8ff28>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 89.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]	0.18
[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f72ad351a20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 89.2 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --overwrite]	0.18
[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f2f74558b70>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 89.1 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]	0.21
[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc2e4ed8a90>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 8.0 kB CPU Usage: 98.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-mac-max 12 --overwrite]	0.17
[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f26cbd9e668>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1468.0 kB CPU Usage: 89.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]	0.18
[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f4686758a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 99.2 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-distance 500 --overwrite]	0.21
[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f91344c8d68>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]	0.18
[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fbfecd43438>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 784.0 kB CPU Usage: 95.4 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]	0.18
[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fce74821a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 89.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]	0.18
[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f5fd1148a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]	0.19
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc109a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 760.0 kB CPU Usage: 99.0 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]	0.19
[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f784d042a20>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 89.0 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]	0.19
[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fb8e9bee198>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 89.4 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]	0.20
[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa5e440f9b0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1200.0 kB CPU Usage: 89.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]	0.20
[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f734cd0ca58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 956.0 kB CPU Usage: 89.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]	0.21
[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f8f496f7b38>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1208.0 kB CPU Usage: 59.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]	0.31
[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f0c29068518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 89.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-maf-max 0.3 --overwrite]	0.28
[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f948e4965f8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1468.0 kB CPU Usage: 99.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]	0.15
[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fb8e80a7518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-include-info DB --overwrite]	0.16
[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f2f74571668>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-mac-max 12 --overwrite]	0.18
[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f7274d754e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 99.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-distance 500 --overwrite]	0.15
[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f8f4970f630>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 88.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]	0.18
[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f91344f75c0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 764.0 kB CPU Usage: 89.2 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]	0.23
[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f39f1f57a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 8.0 kB CPU Usage: 99.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]	0.22
[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1b3dc63b00>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 8.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-distance 500 --overwrite]	0.15
[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f4686777518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-exclude-info H2 --overwrite]	0.18
[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f39f1f1a550>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1200.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-mac-min 8 --overwrite]	0.22
[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1b3dc774e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 59.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]	0.19
[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc9f8df6518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 956.0 kB CPU Usage: 94.7 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]	0.18
[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f7f0125d4e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 99.4 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --overwrite]	0.18
[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fef393d2b70>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 89.5 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-include-info DB --overwrite]	0.17
[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fbb1fea94e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 140.0 kB CPU Usage: 97.6 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]	0.25
[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62f98ca470>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]	0.24
[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa6d1b3d470>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1208.0 kB CPU Usage: 99.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]	0.22
[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fd7dce64518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-include-info DB --overwrite]	0.17
[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f4686758b70>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]	0.25
[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa05689e550>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 1204.0 kB CPU Usage: 89.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]	0.18
[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9b5a3d438>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]	0.19
[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f72ad3724e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 99.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]	0.11
[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f7274d53b70>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]	0.11
[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc2e4ef4550>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]	0.15
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc12a518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]	0.10
[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f734cd2b518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]	0.10
[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa49ab26438>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]	0.14
[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1773e6a4a8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]	0.14
[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe532e4d4e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-info H2 --overwrite]	0.20
[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc9f8dd7be0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --overwrite]	0.32
[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f7f012dbba8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]	0.15
[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fd443311d30>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]	0.38
[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc9f8df6cc0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]	0.21
[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f7f0125dc88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]	0.26
[gw34] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1bf07c2588>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]	0.29
[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe344254d30>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]	0.30
[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f58fced9d68>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-distance 500 --overwrite]	0.27
[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa34e0ba518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]	0.36
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939fa67d68>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]	0.24
[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f41a5879d30>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]	0.23
[gw34] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1bf07a8b70>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]	0.19
[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f72ad351ba8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]	0.20
[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f0308c4ad30>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]	0.21
[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f8a91969518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]	0.25
[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f5596f7ec50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]	0.31
[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9b5a23b00>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-maf-max 0.3 --overwrite]	0.27
[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f72ad372c88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-info DB --overwrite]	0.31
[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa05687ac18>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]	0.12
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc783518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]	0.10
[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f27c366f518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --overwrite]	0.22
[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fcebf611d68>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-distance 500 --overwrite]	0.25
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc76bb00>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 99.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-maf-min 0.2 --overwrite]	0.25
[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9b5a3dbe0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]	0.25
[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa05689ecf8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]	0.28
[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f784d016518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-exclude-info H2 --overwrite]	0.33
[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f27c36a5b38>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-max 12 --overwrite]	0.31
[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fbb1fe8cba8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]	0.36
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8d95c50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-min 0.2 --overwrite]	0.39
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc109be0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]	0.36
[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f4f0e1b5d30>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]	0.27
[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f91da1c9550>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-max 0.3 --overwrite]	0.27
[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f734cd0cbe0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-min 8 --overwrite]	0.28
[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa6d1b1db38>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --overwrite]	0.27
[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f46882dd898>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-flag s50 --overwrite]	0.30
[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62f98f6b38>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]	0.27
[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f7275e582b0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]	0.30
[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fef3a4d9208>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]	0.30
[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa49ab9bb00>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]	0.27
[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f6ec24dc4e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-distance 500 --overwrite]	0.34
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36b1cf8518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]	0.28
[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f0c29049d30>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]	0.31
[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f5fd1165550>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-mac-max 12 --overwrite]	0.31
[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f784d042b00>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]	0.32
[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f948e47fe10>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --overwrite]	0.26
[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7ff99c29b518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]	0.26
[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f976b75eda0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]	0.27
[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fdc732a44e0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --overwrite]	0.29
[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fbb1fea9c88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]	0.41
[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f26cbd87e80>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]	0.48
[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62f98cac18>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]	0.45
[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1fa098ae48>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]	0.41
[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fbfe0d23518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]	0.49
[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f91da1fcb38>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]	0.45
[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc2e4ed8d30>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]	0.49
[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa6d1b3dc18>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --overwrite]	0.45
[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1773e50b70>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-distance 500 --overwrite]	0.48
[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f5fd1148b38>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]	0.49
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36b1cdfb00>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]	0.51
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc12acc0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --overwrite]	0.50
[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fce74845550>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-info H2 --overwrite]	0.49
[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa49ab26be0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]	0.49
[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f734cd2bcc0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]	0.30
[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe532e85ba8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --overwrite]	0.36
[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fdc73284ac8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]	0.24
[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7ff8bbfcdc50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-distance 500 --overwrite]	0.31
[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fd7dce9cbe0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]	0.24
[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa5e43de4a8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-mac-min 8 --overwrite]	0.22
[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fbfe0d92b00>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-mac-min 8 --overwrite]	0.20
[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe532e4dc88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 216.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]	0.27
[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f2f74558e80>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]	0.28
[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc977022550>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-include-info DB --overwrite]	0.21
[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fce74821b38>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 764.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-include-info DB --overwrite]	0.22
[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1773e6ac50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --overwrite]	0.23
[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f8f496f7e48>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-flag s50 --overwrite]	0.15
[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fd7dce64cc0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-mac-max 12 --overwrite]	0.15
[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa5e440fa90>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]	0.19
[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f39f1f57d68>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]	0.20
[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1b3dc63e10>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]	0.26
[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fb8e808ed68>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]	0.25
[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f91344dfdd8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]	0.13
[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fd443332c50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]	0.41
[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa34e0eda90>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]	0.41
[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f8a9199ca90>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]	0.33
[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe3441d6c50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]	0.19
[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f0308c6bc50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]	0.20
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9f1c50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]	0.13
[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f784d016cf8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --overwrite]	0.11
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9ea588>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-flag s50 --overwrite]	0.10
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9e0630>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]	0.27
[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f5596f9fc88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-include-info DB --overwrite]	0.23
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939fa59e48>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]	0.33
[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fcebf630c50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-include-info DB --overwrite]	0.33
[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f41a589ac50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-info H2 --overwrite]	0.11
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f93a20cecc0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]	0.20
[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f0c29068c50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]	0.26
[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7ff99c2d7a90>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-maf-min 0.2 --overwrite]	0.13
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9e0e10>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-include-info DB --overwrite]	0.13
[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f5fd1165d30>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --overwrite]	0.14
[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fbfe0d23cf8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-maf-max 0.3 --overwrite]	0.14
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9dedd8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-distance 500 --overwrite]	0.16
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc783da0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-mac-min 8 --overwrite]	0.13
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9f1f98>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]	0.17
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8daec88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --overwrite]	0.12
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc72d3c8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]	0.12
[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f6ec24c1a90>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --overwrite]	0.20
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8d45518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-mac-max 12 --overwrite]	0.24
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9eac50>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]	0.17
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc76be48>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-distance 500 --overwrite]	0.13
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939fa67f60>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]	0.14
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8d95c18>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]	0.13
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc7405c0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]	0.21
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36b1cf8da0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]	0.13
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc0d20b8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --overwrite]	0.10
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9d9828>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]	0.21
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc72d278>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]	0.30
[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7ff8bbfeec88>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]	0.19
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9e0860>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]	0.25
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc109da0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]	0.29
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36b1ca53c8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]	0.29
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8d575c0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]	0.42
[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fc976ffeac8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]	0.45
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dedb6320>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]	0.37
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9db3cdf98>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-include-info DB --overwrite]	0.41
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9f4518>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-distance 500 --overwrite]	0.41
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc0e75c0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]	0.41
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36b1cdfe48>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]	0.21
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8d95f60>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]	0.38
[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1773dd7470>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --overwrite]	0.18
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bd212780>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]	0.18
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36b1cbd390>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]	0.22
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc783748>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-exclude-info H2 --overwrite]	0.18
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9f1f28>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]	0.10
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8d577f0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]	0.16
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc0fccf8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 500.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]	0.16
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9ea2e8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]	0.16
[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1773e50a58>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]	0.16
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc740c18>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]	0.16
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36b1ca52e8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]	0.16
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f939f9de7f0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]	0.16
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36c6526208>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]	0.16
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc717b38>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 504.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]	0.22
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8d4bfd0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]	0.17
[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f1773dee320>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 228.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]	0.17
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc0e75f8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]	0.29
[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fa9bc0c8048>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 69.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]	0.29
[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f62dc72d0b8>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 484.0 kB CPU Usage: 79.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]	0.31
[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7fe9d8d45fd0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 140.0 kB CPU Usage: 89.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]	0.31
[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f36b1cf8fd0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 764.0 kB CPU Usage: 99.8 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]	0.29
[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f17759d5f60>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 488.0 kB CPU Usage: 69.9 %
Failed	test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-mac-min 8 --overwrite]	0.31
[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3 E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...] assert 1 == 0 + where 1 = <subprocess.Popen object at 0x7f93a0b048d0>.returncode ----------------------------- Captured stdout call ----------------------------- Memory Usage: 232.0 kB CPU Usage: 79.9 %

Result

Test

Duration

Links

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-distance 500 --overwrite]

0.14

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939fa67a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 83.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --overwrite]

0.12

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd4433119e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 87.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-info H2 --overwrite]

0.14

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a5866d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-max 0.3 --overwrite]

0.22

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d84c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.16

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9f1588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 224.0 kB CPU Usage: 89.8 %

Failed

0.16

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443332518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-max 12 --overwrite]

0.21

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c4aa20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.23

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1b59e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1968.0 kB CPU Usage: 99.7 %

Failed

0.22

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f012dba20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.3 %

Failed

0.21

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef3b955f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 87.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-info DB --overwrite]

0.20

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f71c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 3624.0 kB CPU Usage: 99.6 %

Failed

0.20

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa098ab38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-min 0.2 --overwrite]

0.21

[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe3442549e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.4 %

Failed

0.21

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8dd7a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.22

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b750f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.20

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fced9a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa34e0eda20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.24

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfbcc88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-min 8 --overwrite]

0.20

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf611a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.6 %

Failed

0.13

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe8ca20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw34] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1bf07a8a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 88.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.19

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8dae4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.27

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a589a518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --overwrite]

0.12

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c6b550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.7 %

Failed

0.15

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef393ed4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.13

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f9f4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.13

[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe3441d6518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.13

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfee4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Failed

0.22

[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8a9199ca20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

0.13

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1fca58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-flag s50 --overwrite]

0.13

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c290499e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.1 %

Failed

0.14

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fce9d588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.14

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5a0fdd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.14

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b77f588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 97.5 %

Failed

0.13

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c36a5a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.14

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05687aa90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.15

[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62f98f69b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.16

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc76ba20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Failed

0.25

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1b1d9b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Failed

0.18

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1d6518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.7 %

Failed

0.14

[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f26cbd87b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --overwrite]

0.13

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa09a1630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.18

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e85a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.15

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf630588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.17

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e46fd68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 86.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.18

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cdfa20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.2 %

Failed

0.18

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce9ca58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.1 %

Failed

0.18

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d53a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 94.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.18

[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fdc758c1390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 98.1 %

Failed

0.19

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976ffea58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.6 %

Failed

0.18

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e509e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.1 %

Failed

0.18

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99e9125f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.19

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec4aff550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Failed

0.19

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab8ff28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.18

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad351a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --overwrite]

0.18

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f74558b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Failed

0.21

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ed8a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 98.9 %

Failed

0.17

[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f26cbd9e668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1468.0 kB CPU Usage: 89.6 %

Failed

0.18

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686758a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.2 %

Failed

0.21

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344c8d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 69.8 %

Failed

0.18

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfecd43438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 784.0 kB CPU Usage: 95.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.18

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74821a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.5 %

Failed

0.18

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd1148a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc109a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.0 %

Failed

0.19

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d042a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.19

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e9bee198>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.20

[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa5e440f9b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.5 %

Failed

0.20

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734cd0ca58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.6 %

Failed

0.21

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496f7b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 59.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.31

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29068518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Failed

0.28

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e4965f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1468.0 kB CPU Usage: 99.5 %

Failed

0.15

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e80a7518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.16

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f74571668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.18

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d754e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Failed

0.15

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f4970f630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.7 %

Failed

0.18

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344f75c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.23

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f57a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.6 %

Failed

0.22

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc63b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Failed

0.15

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686777518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.18

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f1a550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

0.22

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc774e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 59.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.19

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8df6518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 94.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.18

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f0125d4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --overwrite]

0.18

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef393d2b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.17

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fea94e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 97.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.25

[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62f98ca470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.24

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1b3d470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.22

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce64518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.17

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686758b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.25

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05689e550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.18

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5a3d438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.19

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad3724e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.11

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d53b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.11

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ef4550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.15

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc12a518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]

0.10

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734cd2b518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.10

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab26438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.14

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e6a4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.14

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e4d4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-info H2 --overwrite]

0.20

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8dd7be0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.32

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f012dbba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.15

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443311d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.38

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8df6cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.21

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f0125dc88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.26

[gw34] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1bf07c2588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.29

[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe344254d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.30

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fced9d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.27

[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa34e0ba518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.36

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939fa67d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.24

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a5879d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.23

[gw34] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1bf07a8b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.19

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad351ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.20

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c4ad30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.21

[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8a91969518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.25

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f7ec50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.31

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5a23b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.27

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad372c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-info DB --overwrite]

0.31

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05687ac18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.12

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc783518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.10

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c366f518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.22

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf611d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.25

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc76bb00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

0.25

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5a3dbe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.25

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05689ecf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.28

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d016518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.33

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c36a5b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-max 12 --overwrite]

0.31

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe8cba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.36

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d95c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-min 0.2 --overwrite]

0.39

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc109be0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.36

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1b5d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.27

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1c9550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-max 0.3 --overwrite]

0.27

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734cd0cbe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-min 8 --overwrite]

0.28

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1b1db38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Failed

0.27

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f46882dd898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-flag s50 --overwrite]

0.30

[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62f98f6b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.27

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7275e582b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.30

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef3a4d9208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.30

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab9bb00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.27

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec24dc4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.34

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cf8518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.28

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29049d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Failed

0.31

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd1165550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.31

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d042b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.32

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e47fe10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.26

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c29b518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.26

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b75eda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

0.27

[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fdc732a44e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --overwrite]

0.29

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fea9c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.41

[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f26cbd87e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.48

[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62f98cac18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.45

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa098ae48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.41

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d23518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.49

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1fcb38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.45

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ed8d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.49

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1b3dc18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --overwrite]

0.45

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e50b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-distance 500 --overwrite]

0.48

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd1148b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.49

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cdfb00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.51

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc12acc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --overwrite]

0.50

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74845550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-info H2 --overwrite]

0.49

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab26be0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.49

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734cd2bcc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.30

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e85ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --overwrite]

0.36

[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fdc73284ac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.24

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfcdc50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-distance 500 --overwrite]

0.31

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce9cbe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.24

[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa5e43de4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.22

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d92b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e4dc88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.27

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f74558e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.28

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc977022550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --filter-include-info DB --overwrite]

0.21

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74821b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-include-info DB --overwrite]

0.22

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e6ac50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.23

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496f7e48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.15

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce64cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.15

[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa5e440fa90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.19

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f57d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.20

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc63e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.26

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e808ed68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.25

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344dfdd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.13

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443332c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.41

[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa34e0eda90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.41

[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8a9199ca90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.33

[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe3441d6c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.19

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c6bc50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.20

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9f1c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.13

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d016cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --overwrite]

0.11

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9ea588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.10

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9e0630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.27

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f9fc88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.23

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939fa59e48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.33

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf630c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.33

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a589ac50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.11

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f93a20cecc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]

0.20

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29068c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.26

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c2d7a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.13

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9e0e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.13

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd1165d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --overwrite]

0.14

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d23cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.14

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9dedd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc783da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.13

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9f1f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.17

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8daec88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.12

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72d3c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.12

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec24c1a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --overwrite]

0.20

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d45518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.24

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9eac50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.17

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc76be48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.13

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939fa67f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.14

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d95c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.13

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7405c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.21

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cf8da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.13

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0d20b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-flag q10 --overwrite]

0.10

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9d9828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.21

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72d278>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.30

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfeec88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.19

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9e0860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.25

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc109da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.29

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1ca53c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.29

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d575c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.42

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976ffeac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Failed

0.45

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dedb6320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Failed

0.37

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9db3cdf98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.41

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9f4518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.41

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0e75c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.41

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cdfe48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.21

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d95f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.38

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd7470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

0.18

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bd212780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.18

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cbd390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.22

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc783748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.18

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9f1f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.10

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d577f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.16

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0fccf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Failed

0.16

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9ea2e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.16

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e50a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

0.16

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc740c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.16

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1ca52e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9de7f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]

0.16

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36c6526208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc717b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.22

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d4bfd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]

0.17

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dee320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.17

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0e75f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.29

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0c8048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Failed

0.29

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72d0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.31

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d45fd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.31

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cf8fd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.29

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f17759d5f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.31

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f93a0b048d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.21

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7474a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.21

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cbdba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.21

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0d2898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Failed

0.21

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f177593c908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

0.21

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8daea90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.21

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939fa67ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.11

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1ca0b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dee9b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f93a07cba58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.12

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc76bb38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.12

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc12aa90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.18

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d95b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.10

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cdfa20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.13

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dc8630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.12

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc783128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.13

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc109a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.11

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ef4da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d46668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.14

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e91470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.18

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7119e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.18

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd77f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.12

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d576a0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.17

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0b4470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.21

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1c96160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

0.10

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0e7780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.10

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1c8d208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e86588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e6a828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d4bdd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.11

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc717160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e50cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

0.19

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0eed68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Failed

0.19

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d72940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.20

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cf8940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.19

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72dcc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.19

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4eb35c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.10

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8daeef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dbc5c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Failed

0.11

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0d27b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.34

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc740f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.35

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cbdda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.25

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc12aac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.37

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e6a5d978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.27

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9da8de6a0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.11

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dd7832b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0c83c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.14

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d985df60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.14

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ed8c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.13

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dd4a2d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.11

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0b4f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d95cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-min 8 --overwrite]

0.12

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4eb3358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

0.11

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc711390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc109fd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-max 12 --overwrite]

0.12

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e865f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.13

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8daea58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.11

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72dda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc12a588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d461d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.20

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e91ef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.17

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc76bcf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 69.9 %

Failed

0.17

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0ee710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.11

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d72e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ef49e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.18

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc740a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.14

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d459b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.12

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ed89e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.17

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0d2b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.11

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7834e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.11

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bcbc2cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.12

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d4b1d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.11

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d3bb38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.12

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc109eb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.18

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e8d400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Failed

0.12

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc726eb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.11

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4eb3e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8daeac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0c5f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc711048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Failed

0.17

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d72198>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

0.16

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc12aa20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.30

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc717358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

0.31

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e7e9b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.14

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d57eb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.14

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0eeeb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.10

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72d4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Failed

0.21

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0d26d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

0.21

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e915c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.13

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ef4e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Failed

0.24

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc747588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Failed

0.16

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0e7940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

0.10

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e86c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.10

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dd8c03c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.26

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bcbc2b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.19

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e8d4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.20

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7407f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.15

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc76be80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0b4940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.16

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e59f6518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.24

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc783eb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.23

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e7ec50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.14

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72d588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

0.15

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ed8cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.10

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7264e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.10

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e86f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.11

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dd4b3a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ef4978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.15

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc740978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.15

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ea0240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.11

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa0568380b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-flag s50 --overwrite]

0.11

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05687add8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-info DB --overwrite]

0.10

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05685b5f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-info H2 --overwrite]

0.12

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa0579680f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-min 0.2 --overwrite]

0.15

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa058ebf470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-max 0.3 --overwrite]

0.38

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05685bba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-min 8 --overwrite]

0.12

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa056831b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-distance 500 --overwrite]

0.10

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f4970fcf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-max 12 --overwrite]

0.11

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa0568387b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --overwrite]

0.11

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496b5668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-distance 500 --overwrite]

0.16

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05689e278>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.11

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f5df63208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --overwrite]

0.15

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05687ab00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

0.17

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496f7f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.15

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05685d748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.18

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a5860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.11

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05685b4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.11

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05682ada0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496b5ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.15

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f4970f1d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.28

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa0568385c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.17

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496d41d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.22

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496f7ef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.42

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05689ed30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.37

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a18d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

0.25

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05687add8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

0.40

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa0579680f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --overwrite]

0.48

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a5e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.49

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dee828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --overwrite]

0.24

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab1e4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

0.15

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa0575a2cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

0.12

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a8ac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.13

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e80a7cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.12

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab9bfd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.12

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dc8a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --overwrite]

0.33

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05682a128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.30

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8066518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

0.30

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f4970f198>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.30

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49bcdea90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Failed

0.30

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd3ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.14

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd1400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.15

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496d4b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.14

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e804b518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.17

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa056831e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.15

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49d1e3da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

0.16

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dee908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab15b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.24

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8068588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.24

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa056838e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.35

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496b5eb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.28

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e50e48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.35

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab9bf98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.42

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05685ddd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.50

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8ea444320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.54

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1774ebaf60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

0.64

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f4bd36f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

0.39

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05689ef98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.32

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e808ea58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.53

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab26e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.11

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f17747c43c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Failed

0.11

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f49f1bda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Failed

0.16

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496f7908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.17

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dc8128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.20

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8068978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.21

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa0568267f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.21

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab0e470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.25

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a5668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.25

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e804b9e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

0.24

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05682a6d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.24

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd14e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.24

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab1e4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

0.10

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496b5a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.33

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8066080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.33

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa056831550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.35

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab1d518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

0.25

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496d4a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.36

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dee780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e80a7dd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.30

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496b8390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.22

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e808ef98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

0.30

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e6a0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.31

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab15940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.13

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd7710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.23

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc977022cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.13

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8037780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.13

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a8278>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.11

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dbcf98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f7f358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8068518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.12

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f7b358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Failed

0.13

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dc85f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.12

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e806dac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.13

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1ae4080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.15

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f6a470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Failed

0.15

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd1940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Failed

0.15

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8066588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-min 0.2 --overwrite]

0.18

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc97801eb70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.32

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd7c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.32

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e80a7c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-info H2 --overwrite]

0.11

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1c9c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-max 0.3 --overwrite]

0.15

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc978b6b208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.17

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d45b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.20

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f17747c4278>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-min 8 --overwrite]

0.19

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f6a208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.21

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e804b4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.14

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7115c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --overwrite]

0.15

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf7e518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.9 %

Failed

0.14

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e50f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-max 12 --overwrite]

0.12

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f7b470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.19

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d95be0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.21

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c366fda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.24

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8037470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.22

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1d6c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.25

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfcdeb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.25

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7838d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-maf-max 0.3 --overwrite]

0.27

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1bf358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.19

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f7fbe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

0.31

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dee9e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.17

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0c5ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-mac-min 8 --overwrite]

0.15

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1fce80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.12

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc977022a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.27

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b77f470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf97518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.21

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e88d4710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.16

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72d710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

0.12

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74845d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.10

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d3b518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dbcdd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bd006860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e808ed30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976ffefd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.17

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc109cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.11

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe14198>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce747ef2b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.10

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d986f630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e6a0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e80682e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.18

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfcdf60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --overwrite]

0.17

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d57128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.19

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe8cb38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6e45c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

0.19

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74821e48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.24

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd77b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.24

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e804bd68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --overwrite]

0.17

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1785c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 79.8 %

Failed

0.17

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfee710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.20

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c3664320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.19

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d4b5f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bcbd5668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.32

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf97668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.31

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e80a7518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.32

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1b5e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

0.21

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe25550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --filter-include-info DB --overwrite]

0.21

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d46ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-min 8 --overwrite]

0.27

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e91860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.15

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8061978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --filter-exclude-info H2 --overwrite]

0.15

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d72390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf8e550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb20f793c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.16

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e177550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.17

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1774680b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e7edd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.16

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0e7c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.14

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74803550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.21

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1ca5518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --overwrite]

0.18

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f04080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Failed

0.23

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf7e710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.23

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd1d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.16

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc711208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.23

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0f1ab470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.11

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c36a5ef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.24

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e806d7b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.11

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f66748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.23

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb224c85f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.23

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4eb3cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.30

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0ee8d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.15

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f7eda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.16

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8037898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Failed

0.16

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe25a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.16

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c366a3c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.16

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f6a898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.17

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dee0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.17

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc76bcf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]

0.17

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfcdc18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.13

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596ef04a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.14

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0b4a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.15

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce747ef780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --filter-mac-min 8 --overwrite]

0.15

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8dae5f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-flag q10 --filter-include-info DB --overwrite]

0.11

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8068c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.12

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1ba550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.11

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c46bc588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.10

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf725c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.14

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce76b9ed30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.15

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1b5e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.28

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dbc898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.23

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0c5240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.23

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5597fe0ef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.18

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e804b0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.23

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfee240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.15

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d5e048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.16

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe0b0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-distance 500 --overwrite]

0.16

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f745714a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-max 0.3 --overwrite]

0.16

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dd4b39e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.11

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0d2b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.16

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f7ef60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344f7c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6d4668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.20

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf97f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.19

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe8c908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.19

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e86b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.20

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8dd7dd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.11

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1bf7f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-max 12 --overwrite]

0.22

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc747a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.21

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c47ea160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.29

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ef4828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.21

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f9ffd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

0.30

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfa1b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.20

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91dc831d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.29

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976c8b4668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.20

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1774e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.30

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344985f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.29

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d775c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.29

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fea9ac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.16

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d986f240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.16

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf7ec88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Failed

0.24

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9fa9486a0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-include-info DB --overwrite]

0.16

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d57b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.25

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dc8860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.25

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976c320208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

0.25

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe0a160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.14

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf8e240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.26

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f745156d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.33

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1ca0d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.33

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8dc6f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.32

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd1898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.34

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1c9828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.36

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976fa1b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.37

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596ef07f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.20

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc77cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

0.31

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e806d898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 79.8 %

Failed

0.37

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe07080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.30

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bc96a0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.36

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d3b9e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.31

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc12a748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.32

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72d080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.38

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce748456d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d77390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.20

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e6a7f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.14

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74803cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-min 8 --overwrite]

0.15

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8dae748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.8 %

Failed

0.15

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc76ba90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --filter-include-info DB --overwrite]

0.16

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc255f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.16

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f7f6d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.15

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe25080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.15

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf729e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.20

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c366f748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.13

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f913448b630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce747dfd68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-max 12 --overwrite]

0.11

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d4bba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.21

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1774f0b4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.21

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b75ee10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.20

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc53cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc977022da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.21

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f7450e710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.23

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bc72a4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-distance 500 --overwrite]

0.12

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d84d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.12

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344ae6a0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.17

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1bab70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ed8cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.2 %

Failed

0.13

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0c81d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-info DB --overwrite]

0.15

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e172278>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.15

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d985dc18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.23

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d4fac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.24

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe14860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.4 %

Failed

0.19

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc63ef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.15

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfcdd68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.19

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f7bb70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.19

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596efd828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.16

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74821a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.16

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cf8da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.21

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bcbd5710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.11

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5b95c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.18

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc717ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.18

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d459b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.23

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc97803a748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.17

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc109cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.18

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cdfa58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.25

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe0be48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.25

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf8ed30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.15

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91354868d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.15

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1adb38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.15

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf611e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.16

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f7451b710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.16

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e5989278>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.16

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d46b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.16

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c366ab70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Failed

0.13

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf97da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.20

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc98404fa90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5d9588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.27

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fea95f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.28

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f46867114a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.33

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b28d8358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 948.0 kB CPU Usage: 89.6 %

Failed

0.33

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc25dd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.33

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91414faa90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Failed

0.28

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f17747c4278>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-max 0.3 --overwrite]

0.21

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e178e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.29

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f040f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.29

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d5e908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.25

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8dae1d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.26

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f76ba55c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-info H2 --overwrite]

0.26

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e80a7c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.24

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6c5eb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.24

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfee0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.25

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dd4b3c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.23

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc977825390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.22

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcec1177780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.33

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c3656828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

0.16

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe8cc50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --overwrite]

0.17

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bd1fa240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.24

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce7479c240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.24

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e915f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.18

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976fa1ac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Failed

0.27

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1bfba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.28

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d986fcc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.28

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1c965c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.23

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b77ffd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.18

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb2056d898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-min 8 --overwrite]

0.28

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1d68d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcecc63fa90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.28

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd77f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.25

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d00a400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.26

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443292550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.29

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c36a5f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.35

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf87898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

0.35

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc740780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.29

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0c5d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.37

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c28ff6550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Failed

0.19

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d042c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --filter-exclude-info H2 --overwrite]

0.31

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f7ea58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 0.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.20

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443311ef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.19

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf7e080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Failed

0.19

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29049e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.20

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c36610b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.22

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f012550f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --filter-distance 500 --overwrite]

0.36

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc39ef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 0.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-max 0.3 --overwrite]

0.36

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e88e7518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 10.0 %

Failed

0.36

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f6a0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 10.0 %

Failed

0.35

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5d97f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 10.0 %

Failed

0.36

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6e4eb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 9.9 %

Failed

0.24

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0b4080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --overwrite]

0.23

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686710898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.37

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce747ff518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 0.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.37

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c16550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 0.0 %

Failed

0.35

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d3bf98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 9.9 %

Failed

0.36

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd3b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 10.0 %

Failed

0.41

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb219ec908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 10.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --overwrite]

0.11

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d00e278>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.19

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8df6a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 69.9 %

Failed

0.22

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d72b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.22

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc1dda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.22

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6cd128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.24

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc747978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --overwrite]

0.16

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cbd2e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.27

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c3653240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.16

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344f7358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.23

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c4aef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.18

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fea9ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.29

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29029550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-distance 500 --overwrite]

0.18

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1b5b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.24

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686738518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Failed

0.21

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd1160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.24

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5d3ac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.24

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f66a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.29

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf72978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.18

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef39387470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-flag s50 --overwrite]

0.19

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784e005d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.11

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc77240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.17

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6d4b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.16

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a5833390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.24

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e507b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.25

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe07588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.25

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5b9da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.25

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1b1df98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-max 12 --overwrite]

0.27

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44327a5c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.18

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f012dbda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.17

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e44400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.25

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf8e588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.25

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c2abaf3c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Failed

0.25

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308bfa550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.26

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc72d8d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.25

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f468782a358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.17

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab02438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.17

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f1a940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Failed

0.14

Failed

0.27

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d45908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.24

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f7bbe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.27

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1c2470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.13

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e88d4908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a5879e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.18

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8dd7a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Failed

0.13

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf630128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]

0.13

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab34c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.0 %

Failed

0.13

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf87908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.4 %

Failed

0.14

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dc8fd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.14

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c29bc88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-flag s50 --overwrite]

0.12

[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f26cbd9e5c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Failed

0.14

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe0ba90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.13

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc783160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Failed

0.14

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1aff2b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.14

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1fcbe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.0 %

Failed

0.14

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f89dd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.14

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d577f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.15

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596eef1d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-max 0.3 --overwrite]

0.16

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b59a24a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.16

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce5c0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.14

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd444459e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.35

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344aeac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-info DB --overwrite]

0.33

[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f26cbcff668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --overwrite]

0.35

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6eacc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.39

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef39398898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.33

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d3b240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.33

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe0ae48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.36

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f74babf28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --overwrite]

0.34

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1c9d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.35

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c366f278>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.33

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc977022940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.34

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d2bac2e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.34

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e6afd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

0.49

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc11860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Failed

0.48

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f17550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --overwrite]

0.34

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd444446940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.35

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c296320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --overwrite]

0.45

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8037b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.35

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.35

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab0e4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.35

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1ca5748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-include-info DB --overwrite]

0.34

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec24dcc18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.49

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e85b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.35

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e16a7b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.35

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7408d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.35

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfcdb70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.27

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fce9d978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 69.9 %

Failed

0.40

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d43400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.36

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d1a208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-info H2 --overwrite]

0.44

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e7e9e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.8 %

Failed

0.21

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49d1e3da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

0.22

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f035c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.22

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dd6a87f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.23

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe25208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.23

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef3939b208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.23

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec2483320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.22

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e177cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.22

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976fa1908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-min 0.2 --overwrite]

0.22

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc25390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.27

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c290497f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.15

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f017c2d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

0.22

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c3648f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 99.7 %

Failed

0.23

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e80613c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.23

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bc5ecf28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-min 0.2 --overwrite]

0.15

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e59f6ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.27

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d2f470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.22

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f74571c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.24

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cf8d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 552.0 kB CPU Usage: 79.9 %

Failed

0.24

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d84d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.22

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1d5470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.23

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d92c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.24

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6cab00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.22

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e433c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.28

[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa34e0bac88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.22

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d77470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.22

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5c5470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.16

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fdf6f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.32

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0e7a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Failed

0.19

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fea94a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Failed

0.13

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd7940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.34

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1ad160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

0.35

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe5349f2cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.34

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a1588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

0.29

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734ccd5208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.34

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9dcb8e0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-max 0.3 --overwrite]

0.31

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dbdc550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --filter-include-info DB --overwrite]

0.14

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9e0d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1216.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --overwrite]

0.32

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfeddd4a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.29

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686744e48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.15

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dd4b3358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

0.32

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5d93c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.15

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec24c1ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.32

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf7e390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.33

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d53d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.34

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f6a4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

0.12

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f89d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.0 %

Failed

0.12

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1bfb00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-min 0.2 --overwrite]

0.28

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d5d5940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --overwrite]

0.13

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d3ed3ac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.34

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49bb5e438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.13

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab263c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.18

[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fdc732a4cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-distance 500 --overwrite]

0.16

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5a23f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 476.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.18

[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62f98be470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.32

[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe3441d1518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.19

[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fdc73208320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Failed

0.21

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef3aff5208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Failed

0.18

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734cd0cac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-min 8 --overwrite]

0.19

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ed8b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --overwrite]

0.19

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c2d7dd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.20

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f012c6b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --overwrite]

0.19

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe07320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.6 %

Failed

0.19

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b77f0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf59ff28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.22

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f9134498860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Failed

0.18

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc1df60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Failed

0.20

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bc72ac88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4688322dd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-max 0.3 --overwrite]

0.19

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d00ec18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.22

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d0a898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

0.18

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc109a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c3664400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Failed

0.14

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce9cac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.7 %

Failed

0.14

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0309963320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.7 %

Failed

0.14

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab02518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.15

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc76bb38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.16

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976ffea90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --overwrite]

0.16

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5997080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.14

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d94644e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.0 %

Failed

0.18

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5b9b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 86.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-min 8 --overwrite]

0.26

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d0429e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.26

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c366aac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.26

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686710b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 88.9 %

Failed

0.25

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f9feb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.2 %

Failed

0.22

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf8e5f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.19

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1b1db38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-max 12 --overwrite]

0.26

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e4969e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.1 %

Failed

0.17

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b6b24b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.20

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab1ef28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa5e43dec88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1ba358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-flag s50 --overwrite]

0.22

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe0b160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Failed

0.20

[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa34e0ad320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 99.8 %

Failed

0.13

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad31a0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e808ee10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Failed

0.18

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc783a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

0.26

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f7451b080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.3 %

Failed

0.25

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d5eb00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --overwrite]

0.21

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce6f588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.9 %

Failed

0.20

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443332828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --overwrite]

0.25

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fce905c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --overwrite]

0.21

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bcbc2ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.22

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e18f4e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.3 %

Failed

0.20

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf6303c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.25

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc977631828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.14

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc77d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.7 %

Failed

0.14

[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa34e0eddd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Failed

0.14

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f74515c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Failed

0.14

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab9b908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.5 %

Failed

0.14

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5a0fc88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 98.1 %

Failed

0.13

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef3b9554a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-distance 500 --overwrite]

0.14

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e4365f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 87.9 %

Failed

0.18

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd110a240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.18

[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8a91969c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.5 %

Failed

0.18

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dfd9b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 100.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.19

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbff55f5208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 86.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.20

[gw34] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1bf07c2da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.19

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9deb00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.7 %

Failed

0.21

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fce8f5f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.5 %

Failed

0.18

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe5354e2a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef3939b828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.4 %

Failed

0.18

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab0ef28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 94.7 %

Failed

0.19

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948ffd0c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Failed

0.18

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e80a7080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Failed

0.19

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb1fe0a908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 96.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.18

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc740b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-info DB --overwrite]

0.19

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7ddf544a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 3840.0 kB CPU Usage: 103.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.21

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e178320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Failed

0.20

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686711898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Failed

0.18

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5997e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --overwrite]

0.19

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec247a400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 94.2 %

Failed

0.20

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f913448b630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.8 %

Failed

0.18

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8df64a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 99.1 %

Failed

0.18

[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62f98f6f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.7 %

Failed

0.19

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f7450e048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-info H2 --overwrite]

0.19

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7de9cd4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.7 %

Failed

0.19

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5a23d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.20

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f9490ac4390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.19

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d95d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Failed

0.18

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dd3f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.1 %

Failed

0.18

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cdfb70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 3360.0 kB CPU Usage: 93.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --filter-mac-max 12 --overwrite]

0.20

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9f4908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.5 %

Failed

0.18

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74845470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.5 %

Failed

0.31

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e43a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.5 %

Failed

0.31

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5d32b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 96.0 %

Failed

0.28

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f7450b2e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

0.30

[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62fb49cf28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 87.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.31

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc398d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 98.0 %

Failed

0.18

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f0124ed30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1212.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.29

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1d6630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 97.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.17

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c28d438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.17

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd1148c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.17

[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8a91960320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.27

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da72d8d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Failed

0.19

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29068080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.27

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6e4160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.8 %

Failed

0.20

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d330b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Failed

0.29

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab154e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.7 %

Failed

0.27

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f46867770b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.29

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e436b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 2232.0 kB CPU Usage: 89.8 %

Failed

0.15

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce747d1b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --filter-distance 500 --overwrite]

0.16

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9e1240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.19

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f030a7722e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.28

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc717908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 91.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.31

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc12a630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 98.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.28

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784cff5470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Failed

0.29

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5992438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --overwrite]

0.28

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce6fba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 88.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.30

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad351da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 88.9 %

Failed

0.18

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734cce8400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-info H2 --overwrite]

0.14

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44327ae48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Failed

0.15

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f7452d780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.15

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6c5710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.3 %

Failed

0.15

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8dd7828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.19

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a5c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.19

[gw34] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1bf0768390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Failed

0.19

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5a3d048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 90.4 %

Failed

0.20

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29029978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.20

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686719550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.20

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab34160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.19

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7275dc17f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.20

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce747ef908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.21

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cacf60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 85.1 %

Failed

0.19

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa09a1710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 96.8 %

Failed

0.20

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad315550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 88.7 %

Failed

0.20

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf97908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.21

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e172e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.20

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0ee2b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-min 0.2 --overwrite]

0.18

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44328e940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.17

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e8d9e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 89.6 %

Failed

0.18

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b75ebe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 96.6 %

Failed

0.19

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c36569e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-maf-min 0.2 --overwrite]

0.18

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd1108550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.7 %

Failed

0.18

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e459048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.19

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f468671f240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.5 %

Failed

0.19

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef39398c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.7 %

Failed

0.18

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1c96710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.19

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d016048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.19

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c290019b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.19

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce748031d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 87.6 %

Failed

0.19

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab02a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.0 %

Failed

0.18

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99d213fd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.7 %

Failed

0.19

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734dd7cd30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 78.5 %

Failed

0.18

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5984438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.19

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496b5828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 97.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-maf-max 0.3 --overwrite]

0.19

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443292be0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.19

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e86dd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Failed

0.18

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976c30ffd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 90.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.18

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f74571240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 544.0 kB CPU Usage: 86.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.18

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc11080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 88.7 %

Failed

0.18

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef39387c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.18

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cbd550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.6 %

Failed

0.18

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab1def0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 86.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --overwrite]

0.19

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfa1dd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.18

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c28ff66d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.0 %

Failed

0.18

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686738b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7266d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1716.0 kB CPU Usage: 89.6 %

Failed

0.20

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce7585d0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 86.9 %

Failed

0.18

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c2d7d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.22

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e496748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-mac-max 12 --overwrite]

0.18

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce46438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 3620.0 kB CPU Usage: 99.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.19

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c6b3c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 86.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-min 8 --overwrite]

0.19

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443311d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.19

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e917f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.3 %

Failed

0.19

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976bdea7f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 94.7 %

Failed

0.18

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596ef0668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.7 %

Failed

0.19

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c47ea160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Failed

0.18

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef393ed080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --overwrite]

0.18

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebfbbf908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.19

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0c5828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Failed

0.18

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab1ecc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.18

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd21bf9e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 92.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.19

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1ca5898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.18

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8066320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.19

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c28ffc438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-max 0.3 --overwrite]

0.18

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d05be0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.3 %

Failed

0.18

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c28d518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.4 %

Failed

0.19

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f46866dddd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 99.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.19

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74821828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 88.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.19

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5997f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.19

[gw15] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62fa0b36d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.18

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773e50ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.19

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1ada5f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.22

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc12ab00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.0 %

Failed

0.22

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef393913c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.7 %

Failed

0.26

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6ea048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Failed

0.20

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686711d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.19

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9f1080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.22

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8068908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.0 %

Failed

0.28

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1c2c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 88.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --overwrite]

0.25

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa0908630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Failed

0.22

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab0e128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

0.27

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f744d9e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.21

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fceb45f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-passed --overwrite]

0.27

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e7e9b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 98.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.24

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcec05ba128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.25

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e38748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.21

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c28fee5f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.23

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3e26dcc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.23

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc7118d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.6 %

Failed

0.26

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d45e48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 95.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.20

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74e9ba20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-min 8 --overwrite]

0.21

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d92978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.17

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1ae4780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-mac-max 12 --overwrite]

0.28

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44327b748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.3 %

Failed

0.23

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e78e7f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.7 %

Failed

0.28

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb204622b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 94.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.26

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f216d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.20

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a8f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.22

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b21dd550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.6 %

Failed

0.20

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c284860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

0.17

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f46867774a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 94.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --overwrite]

0.18

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad76bbe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.5 %

Failed

0.18

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef393af0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.17

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cdfa58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Failed

0.18

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab8fe80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.3 %

Failed

0.20

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6c5240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-distance 500 --overwrite]

0.19

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d46898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 94.8 %

Failed

0.19

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc63f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.4 %

Failed

0.19

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e85eb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 98.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.20

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f0124ae80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-min 8 --overwrite]

0.20

[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8a9199cdd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-distance 500 --overwrite]

0.21

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd4433323c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-info DB --overwrite]

0.18

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf87978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --overwrite]

0.21

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784cffa4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --overwrite]

0.21

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f04be0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.5 %

Failed

0.20

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1775a6da20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 96.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.21

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce748038d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.21

[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe344254fd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.9 %

Failed

0.23

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4eb3dd8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.20

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29068b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 91.9 %

Failed

0.22

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c296b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.22

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a5858550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.21

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344b6438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.23

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f107f7518>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-distance 500 --overwrite]

0.19

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9775c5630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 85.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.18

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f31128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.18

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d43da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Failed

0.18

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4688b09128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.5 %

Failed

0.18

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef3939b748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --overwrite]

0.18

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa4a6b42240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.7 %

Failed

0.18

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6e44e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 88.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --overwrite]

0.18

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd4432d2a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 95.6 %

Failed

0.19

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f0125df60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 86.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.20

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b2cd2e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.8 %

Failed

0.20

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e437c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-info H2 --overwrite]

0.19

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf7e898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Failed

0.21

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e4da20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 79.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.19

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce74845f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 90.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --overwrite]

0.18

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c29b780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.20

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29010978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.19

[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa5e43d6400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 95.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.19

[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f26cc296940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.20

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1b3db38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.7 %

Failed

0.19

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ea0978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.3 %

Failed

0.22

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b59a2080>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.19

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fea52fd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-max 12 --overwrite]

0.21

[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8a9197b438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 99.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --overwrite]

0.20

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a6972588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 88.1 %

Failed

0.18

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7276922d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 97.7 %

Failed

0.18

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef393b2d68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.17

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49b07bb70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.3 %

Failed

0.19

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f46900630f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 94.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.18

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d3be10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.18

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44328e0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-info DB --overwrite]

0.18

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e804ba58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.2 %

Failed

0.20

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6cdc88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.20

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f74515ac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 83.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-flag s50 --overwrite]

0.19

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c2990f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Failed

0.17

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a5879a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Failed

0.18

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa1abaeb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Failed

0.18

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e41550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-info DB --overwrite]

0.20

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f012555c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 99.1 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.19

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5597371c88>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.8 %

Failed

0.19

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e5e03da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.18

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce747d1a20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.7 %

Failed

0.19

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1c96c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.21

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c290010b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-include-info DB --overwrite]

0.18

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd3788898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.4 %

Failed

0.16

[gw34] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1bf0b4eba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.1 %

Failed

0.17

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef39387c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.16

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443292710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 92.9 %

Failed

0.20

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad5bd400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.19

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb346ce208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 93.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.18

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6ca240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 98.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --overwrite]

0.19

[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8a9295be80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Failed

0.18

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f012dbcc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.20

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f91c6198>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 85.7 %

Failed

0.18

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a589a320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 99.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.18

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce747ffeb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.18

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dd4b3fd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 98.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --overwrite]

0.18

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1acc390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 93.0 %

Failed

0.18

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f177448cf98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 85.2 %

Failed

0.18

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e59f6908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.18

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9ea160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.19

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f4593b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.20

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec2906358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 78.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.20

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce5c898>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 88.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.20

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734e897d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-min 8 --overwrite]

0.18

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbfee320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --overwrite]

0.20

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44327a390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.19

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686aee8d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 94.8 %

Failed

0.18

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f01296390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.20

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf611a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.6 %

Failed

0.19

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f49b1fcf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.20

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344a07f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 69.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --overwrite]

0.19

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f17747c4320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.20

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a5858668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e876940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 93.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-max-alleles 4 --overwrite]

0.19

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ed8c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 78.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.18

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9e0160>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.4 %

Failed

0.19

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f57d30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 86.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.19

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec4aff198>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.19

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308bfaa90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 83.9 %

Failed

0.20

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce64390>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.19

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc1d0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1212.0 kB CPU Usage: 87.2 %

Failed

0.17

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686758b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.1 %

Failed

0.21

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec247a668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-max-missing 1.0 --overwrite]

0.26

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e91b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-max 12 --overwrite]

0.28

[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f26cbd87e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.20

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab1e0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Failed

0.24

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc0e7908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-chr chr2 --overwrite]

0.23

[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Cannot specify chromosomes to keep and to exclude', 'Traceback (most recent call last):'...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa34e0a4438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.8 %

Failed

0.20

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c04320>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.23

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f31828>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.19

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce9ca90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.32

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fd1ef5c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.31

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f93cec18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Failed

0.17

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686738cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.32

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5d97f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --overwrite]

0.25

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939f9de470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --overwrite]

0.20

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c3c09c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-info DB --overwrite]

0.29

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c28ff61d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 292.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.34

[gw39] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8a9199cd30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 96.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.32

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa056838f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

0.31

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dfd8d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.6 %

Failed

0.22

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef393ed1d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --overwrite]

0.32

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f49f2c1d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-max 12 --overwrite]

0.35

[gw22] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbb2056d940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 98.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-max-alleles 4 --overwrite]

0.37

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa477f048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 69.7 %

Failed

0.29

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc783438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Failed

0.11

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c4add8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-chr chr1 --overwrite]

0.11

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4ef4f60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Failed

0.13

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f035f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --overwrite]

0.20

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec246df60>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.18

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734cd0cfd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.16

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab0e8d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-max-missing 1.0 --overwrite]

0.18

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa09017f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.19

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d00e2e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef39398a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.19

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05685b6d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Failed

0.20

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d534e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw21] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1773dc8630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.20

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce51710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.16

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c36a5940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

0.17

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9d0961208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.16

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5c5c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-chr chr2 --overwrite]

0.12

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4eb3588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.31

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1d6b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.31

[gw50] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fcebf5d35c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.17

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce7479cb38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-chr chr2 --overwrite]

0.18

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Cannot specify chromosomes to keep and to exclude', 'Traceback (most recent call last):'...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f559758e208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-min 0.2 --overwrite]

0.29

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29029c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Failed

0.38

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f17e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-chr chr1 --overwrite]

0.32

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa0908e10>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-max-missing 1.0 --overwrite]

0.39

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f7be48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-chr chr2 --overwrite]

0.18

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Cannot specify chromosomes to keep and to exclude', 'Traceback (most recent call last):'...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f468671f7b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-from-bp 1000000 --overwrite]

0.31

[gw2] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f26cbcf9860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.18

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f4970f5c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.29

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce6f6d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Failed

0.32

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6d4400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.33

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd443304e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-min-alleles 2 --overwrite]

0.30

[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fdc73284da0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Failed

0.32

[gw43] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Require a single chromosome when specifying a range.', 'Traceback (most recent call last...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f6ec2483b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.32

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734ccbfb70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.25

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b598f0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.7 %

Failed

0.24

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e1b5e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-include-chr chr1 --overwrite]

0.24

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f6a438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.17

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1fce80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.17

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d23cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-chr chr2 --overwrite]

0.17

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Cannot specify chromosomes to keep and to exclude', 'Traceback (most recent call last):'...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d042b00>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.21

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44327b2e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-chr chr2 --overwrite]

0.26

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa09a1a58>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-chr chr1 --overwrite]

0.11

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d4fd30>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.19

Failed

0.10

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6ea9e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Failed

0.18

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44385dd68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Failed

0.20

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d0a748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-alleles 4 --overwrite]

0.15

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1c8d668>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-chr chr2 --overwrite]

0.17

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8037208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Failed

0.15

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b6c58d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-chr chr2 --overwrite]

0.26

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Cannot specify chromosomes to keep and to exclude', 'Traceback (most recent call last):'...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1aff860>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.8 %

Failed

0.21

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fce9d8d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-exclude-chr chr2 --overwrite]

0.30

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f66208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.12

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa0575a2f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.12

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c29d5f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.12

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d2fda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Failed

0.27

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa0907eb8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-chr chr1 --overwrite]

0.12

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d19550>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

0.24

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b598ada0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-min-alleles 2 --overwrite]

0.17

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496a1cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

0.16

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f7450e400>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-min-alleles 2 --overwrite]

0.27

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d93b4588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.25

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e172710>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.16

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d5efd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Failed

0.20

[gw36] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fbfe0d1a6d8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-alleles 4 --overwrite]

0.16

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f1a748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Failed

0.15

[gw51] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0308c0a780>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-chr chr1 --overwrite]

0.16

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd4432d2630>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-chr chr2 --overwrite]

0.20

[gw42] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Cannot specify chromosomes to keep and to exclude', 'Traceback (most recent call last):'...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc976f7f8d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

0.21

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1ac32b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Failed

0.25

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fceb43c8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

0.20

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f0124ed68>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-max-missing 1.0 --overwrite]

0.17

[gw12] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4686710240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-min-alleles 2 --overwrite]

0.21

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e7e588>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-max-alleles 4 --overwrite]

0.14

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8dae1d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.32

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a582f9e8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-chr chr2 --overwrite]

0.32

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1d5240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Failed

0.31

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c28d940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-max-missing 1.0 --overwrite]

0.30

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e8555470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-missing 1.0 --overwrite]

0.33

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1ca56a0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.38

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa098aa20>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-max-alleles 4 --overwrite]

0.53

[gw3] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f8f496b5f98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.54

[gw48] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe344fcf358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

0.44

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f0124a0b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.51

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e18f8d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

0.46

[gw8] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f976b994940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-chr chr2 --overwrite]

0.44

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44328e0f0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.45

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d43cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

0.44

[gw20] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa6d1adada0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

0.44

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fce90cc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-max-missing 1.0 --overwrite]

0.16

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29036f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-min-alleles 2 --overwrite]

0.50

[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa5e440fc18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-min-alleles 2 --overwrite]

0.22

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1cf8358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Failed

0.22

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1ad9b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

0.67

[gw6] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f2f7452def0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-chr chr2 --overwrite]

0.23

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Cannot specify chromosomes to keep and to exclude', 'Traceback (most recent call last):'...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734ccd5908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Failed

0.21

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c295af2b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv-file Schweinfurthii.txt --filter-max-alleles 4 --overwrite]

0.21

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b28d85f8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-alleles 4 --overwrite]

0.21

[gw32] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91da1babe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-indv-file Schweinfurthii.txt --overwrite]

0.11

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Could not open Individual file:None', 'Traceback (most recent call last):', ' File "/ho...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e5b358>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-bed chr1_sites.bed --overwrite]

0.18

[gw11] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Multiple --bed/--exclude-bed options can not be used together.', 'Traceback (most recen...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7274d75c18>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-bed chr1_sites.bed --overwrite]

0.48

[gw1] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Multiple --bed/--exclude-bed options can not be used together.', 'Traceback (most recen...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1b3dc25940>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-bed chr1_sites.bed --overwrite]

0.38

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Multiple --bed/--exclude-bed options can not be used together.', 'Traceback (most recen...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e88e7470>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-passed --overwrite]

0.32

[gw4] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f1fa08ea748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.27

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5596f7ecf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-bed chr1_sites.bed --overwrite]

0.27

[gw41] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff99c27d978>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Failed

0.13

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e807ccc0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-bed chr1_sites.bed --overwrite]

0.14

[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Multiple --bed/--exclude-bed options can not be used together.', 'Traceback (most recen...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa34e28d6a0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-flag q10 --overwrite]

0.14

[gw16] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa05687aef0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-passed --overwrite]

0.17

[gw23] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd7dce5f4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.18

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1ca0048>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --filter-include-flag q10 --overwrite]

0.18

[gw7] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f39f1f57ac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-bed chr1_sites.bed --overwrite]

0.21

[gw28] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Multiple --bed/--exclude-bed options can not be used together.', 'Traceback (most recen...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f72ad351908>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-bed chr1_sites.bed --overwrite]

0.18

[gw55] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Multiple --bed/--exclude-bed options can not be used together.', 'Traceback (most recen...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f58fce8f748>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Failed

0.21

[gw45] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f0c29049b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.30

[gw46] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5597579f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-positions chr1_sites.sites --overwrite]

0.31

[gw37] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f784d060ba8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-flag q10 --overwrite]

0.21

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f939fea2cf8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-bed chr1_sites.bed --overwrite]

0.21

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ['exp_handler - ERROR: Error: Multiple --bed/--exclude-bed options can not be used together.', 'Traceback (most recen...fname_arg + vcftools_call_args, output_format = vcf_args.out_format, output_filename = vcftools_output_filename)', ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef398c0438>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-flag q10 --overwrite]

0.27

[gw18] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa9bc7a8128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-bed chr1_sites.bed --overwrite]

0.27

[gw29] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fce747efe48>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-positions chr1_sites.sites --overwrite]

0.30

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8df6e80>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-bed chr1_sites.bed --overwrite]

0.31

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc740b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-bed chr1_sites.bed --overwrite]

0.21

[gw27] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa5e43dc1d0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-positions chr1_sites.sites --overwrite]

0.27

[gw24] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa49ab26ac8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-min 8 --overwrite]

0.19

[gw40] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fa34eec7b38>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-min 8 --overwrite]

0.18

[gw10] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fef393d2be0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-info DB --filter-distance 500 --overwrite]

0.18

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e15ea90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-distance 500 --overwrite]

0.13

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734cd2b5c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-info DB --filter-mac-min 8 --overwrite]

0.18

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f01275a90>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-max 12 --overwrite]

0.22

[gw5] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f91344f79b0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-max 12 --overwrite]

0.20

[gw52] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f93a20b0b70>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 548.0 kB CPU Usage: 89.9 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-info DB --filter-mac-max 12 --overwrite]

0.22

[gw25] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9b5a3d4a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 92.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-max 12 --overwrite]

0.22

[gw0] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f948e47fda0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-min 0.2 --overwrite]

0.22

[gw17] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc9f8d90be0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.2 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-mac-min 8 --filter-distance 500 --overwrite]

0.21

[gw44] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7ff8bbf725c0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.7 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-min 8 --overwrite]

0.22

[gw47] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f41a5833c50>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-maf-max 0.3 --overwrite]

0.21

[gw53] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fd44327af98>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 87.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-maf-max 0.3 --overwrite]

0.23

[gw30] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f36b1c964e0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-info DB --filter-maf-max 0.3 --overwrite]

0.21

[gw49] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe9d8d57240>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-mac-min 8 --filter-distance 500 --overwrite]

0.23

[gw19] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f734cccf208>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 90.5 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-max 12 --overwrite]

0.23

[gw14] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f7f012557b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 99.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-max 12 --overwrite]

0.23

[gw9] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fb8e88d47b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.3 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-min 0.2 --overwrite]

0.23

[gw31] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fe532e434a8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 756.0 kB CPU Usage: 99.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-max 12 --overwrite]

0.23

[gw33] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fdc7333dfd0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 93.6 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-mac-min 8 --filter-mac-max 12 --overwrite]

0.23

[gw26] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f62dc6e4f28>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 82.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-info DB --filter-maf-min 0.2 --overwrite]

0.23

[gw35] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f27c366f128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.0 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-min 8 --overwrite]

0.23

[gw13] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7fc2e4e8dbe0>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 90.4 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-min 8 --overwrite]

0.21

[gw54] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.kept.bed'", 'Traceback (most recent call last):...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f4f0e16a128>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.8 %

Failed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-max 12 --overwrite]

0.23

[gw38] linux -- Python 3.6.3 /opt/rh/rh-python36/root/usr/bin/python3
E AssertionError: ["exp_handler - ERROR: [Errno 2] No such file or directory: 'chr11_vcf.removed.bed'", 'Traceback (most recent call las...ine 150, in cvt_vcftools_site_to_bed', " if 'CHROM' not in vcftools_out_str or 'POS' not in vcftools_out_str:", ...]
assert 1 == 0
+ where 1 = <subprocess.Popen object at 0x7f5fd11087b8>.returncode
----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 90.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 544.0 kB CPU Usage: 100.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 92.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-distance 500 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 544.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-maf-min 0.2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 100.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 748.0 kB CPU Usage: 88.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 92.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 548.0 kB CPU Usage: 96.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1220.0 kB CPU Usage: 92.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 292.0 kB CPU Usage: 95.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 92.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 92.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 544.0 kB CPU Usage: 98.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1464.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 91.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 95.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1212.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 73.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-from-bp 1000000 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 256.0 kB CPU Usage: 91.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-info DB --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 88.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 96.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 81.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 98.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 74.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3096.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 92.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-mac-min 8 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 78.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-flag s50 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1468.0 kB CPU Usage: 93.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 69.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 96.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 544.0 kB CPU Usage: 102.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 548.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-info H2 --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 93.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 59.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --filter-mac-max 12 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-mac-max 12 --overwrite]

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-flag s50 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-to-bp 2000000 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-min 0.2 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --filter-include-info DB --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-max 0.3 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-min 8 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-max 12 --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --filter-exclude-info H2 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-info H2 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --filter-distance 500 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-info DB --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-distance 500 --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-info H2 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-distance 500 --overwrite]

0.89

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-flag q10 --overwrite]

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-max 12 --overwrite]

1.00

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --filter-mac-min 8 --overwrite]

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-include-info DB --overwrite]

1.01

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-info DB --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-passed --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 59.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-maf-max 0.3 --overwrite]

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

1.05

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.99

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --overwrite]

0.92

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-maf-min 0.2 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.92

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-flag s50 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-flag q10 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-distance 500 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-to-bp 2000000 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-flag q10 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-min 8 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-info DB --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-flag s50 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 480.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-from-bp 1000000 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-min 8 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-info H2 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 948.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-distance 500 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-max 0.3 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-max 12 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.4 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.7 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.5 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 88.5 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.5 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.6 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.0 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2832.0 kB CPU Usage: 99.4 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.1 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.2 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.7 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.2 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.6 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-passed --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.7 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 97.0 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.7 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 98.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 88.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1968.0 kB CPU Usage: 99.6 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 98.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.2 %

Passed

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 96.1 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.1 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 88.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-min 0.2 --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.4 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.1 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 97.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-flag s50 --overwrite]

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-distance 500 --overwrite]

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 91.1 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.1 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 100.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 98.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 91.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.0 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 92.1 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-info H2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-max 12 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.7 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 88.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-info DB --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.4 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 87.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1216.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-min 8 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 472.0 kB CPU Usage: 88.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 85.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 548.0 kB CPU Usage: 100.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 101.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 88.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.3 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3360.0 kB CPU Usage: 99.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 101.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 93.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-flag s50 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 94.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 88.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 87.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 101.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-min 8 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 95.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 83.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 292.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1968.0 kB CPU Usage: 87.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.4 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 85.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.1 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.6 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3624.0 kB CPU Usage: 99.5 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 252.0 kB CPU Usage: 96.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3360.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 99.1 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.4 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 87.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 93.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 94.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 98.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-max 12 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 87.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 88.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 756.0 kB CPU Usage: 89.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 92.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 98.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 95.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1464.0 kB CPU Usage: 99.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 94.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3356.0 kB CPU Usage: 99.6 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 92.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 88.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 256.0 kB CPU Usage: 99.1 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 95.3 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 86.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 948.0 kB CPU Usage: 91.9 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.0 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 99.2 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2832.0 kB CPU Usage: 87.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1968.0 kB CPU Usage: 99.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 88.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3624.0 kB CPU Usage: 102.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 86.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 98.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 97.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 93.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 256.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.3 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 77.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3360.0 kB CPU Usage: 104.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 79.6 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 84.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 96.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 95.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 87.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1968.0 kB CPU Usage: 90.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 95.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 96.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.2 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 78.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.3 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 87.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 86.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 96.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1968.0 kB CPU Usage: 88.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 98.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 98.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 91.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-distance 500 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-info H2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 99.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 88.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 94.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.5 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 85.7 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 94.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 98.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1964.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-include-info DB --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3624.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 96.3 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 98.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2828.0 kB CPU Usage: 99.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 99.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 81.9 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 96.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 86.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1964.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 92.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 136.0 kB CPU Usage: 99.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 95.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3096.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 96.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2572.0 kB CPU Usage: 101.1 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.0 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2572.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2232.0 kB CPU Usage: 99.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 100.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 77.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-flag s50 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 97.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 92.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 96.4 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 90.2 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.5 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-include-info DB --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.4 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-min 8 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 272.0 kB CPU Usage: 92.1 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 69.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.7 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.4 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-distance 500 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 69.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 95.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.2 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 69.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.7 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-info DB --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.4 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-include-info DB --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --filter-mac-max 12 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-distance 500 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.1 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --filter-mac-min 8 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-info DB --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-min 0.2 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-flag s50 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-info H2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 95.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.90

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.4 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-distance 500 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-mac-max 12 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.92

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2832.0 kB CPU Usage: 98.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-max 0.3 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-maf-max 0.3 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-mac-min 8 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-min 0.2 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-info H2 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-flag q10 --filter-distance 500 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-info DB --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-flag s50 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-maf-min 0.2 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.90

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

1.03

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

1.00

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

1.05

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

1.05

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.98

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

1.05

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

1.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

1.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

1.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

1.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

1.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

1.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

1.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

1.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --overwrite]

1.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

1.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

1.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

1.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

1.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

1.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

1.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --overwrite]

1.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --filter-include-info DB --overwrite]

1.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

1.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-distance 500 --overwrite]

1.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

1.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

1.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-to-bp 2000000 --overwrite]

1.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-flag q10 --overwrite]

1.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --filter-distance 500 --overwrite]

1.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

1.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

1.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

1.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

1.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

1.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-min 8 --overwrite]

1.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-flag q10 --filter-include-info DB --overwrite]

1.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

1.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

1.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-from-bp 1000000 --overwrite]

1.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

1.09

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

1.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

1.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-max 0.3 --overwrite]

1.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

1.10

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

1.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

1.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

1.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-max 12 --overwrite]

1.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --filter-exclude-info H2 --overwrite]

1.09

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

1.02

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

1.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

1.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

1.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-maf-max 0.3 --overwrite]

1.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.94

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-distance 500 --overwrite]

0.94

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.87

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

1.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

1.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-info H2 --overwrite]

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-max 12 --overwrite]

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

1.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

1.08

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-info DB --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.93

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

1.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-flag q10 --overwrite]

0.87

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-min 8 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-min 8 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-passed --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-to-bp 2000000 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.86

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-min 0.2 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-flag s50 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-maf-min 0.2 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 59.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-max 0.3 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-max 12 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-distance 500 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-flag s50 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-passed --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.89

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-distance 500 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-max 12 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-min 8 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 78.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-include-info DB --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-include-info DB --overwrite]

0.86

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.91

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.86

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.83

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 76.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.8 %

Passed

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --overwrite]

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-min 8 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-min 0.2 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-info DB --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-distance 500 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-min 0.2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-info H2 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-info DB --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.86

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-min 8 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-max 12 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-distance 500 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-include-info DB --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.86

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-info H2 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-max 0.3 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

0.87

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.87

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-flag s50 --overwrite]

0.95

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-max 0.3 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-max 12 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-min 0.2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-distance 500 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-include-info DB --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-distance 500 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-flag s50 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-max 0.3 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-min 8 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-info H2 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-info DB --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-distance 500 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-max 12 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-max 12 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-min 8 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --overwrite]

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-flag s50 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 59.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 224.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --overwrite]

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-distance 500 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-info DB --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-min 8 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-distance 500 --overwrite]

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

1.04

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

1.09

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-info H2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.95

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-info DB --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --overwrite]

1.10

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-info DB --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --overwrite]

1.10

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

1.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-max 0.3 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --overwrite]

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-distance 500 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-info DB --overwrite]

0.97

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.97

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-maf-min 0.2 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.92

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.97

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-max 12 --overwrite]

1.00

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-max 12 --overwrite]

1.00

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --filter-include-info DB --overwrite]

0.10

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.94

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-info H2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.94

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-max 12 --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

1.03

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-min 0.2 --overwrite]

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-flag s50 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --filter-exclude-info H2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-info H2 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-min 0.2 --overwrite]

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-distance 500 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-min 8 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-max 0.3 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-maf-max 0.3 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-info H2 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-min 8 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-min 0.2 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-info H2 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-min 0.2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-flag s50 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-flag s50 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-mac-min 8 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-max 0.3 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-max 0.3 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --filter-mac-min 8 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-max 12 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-max 12 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-info DB --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-mac-max 12 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-include-info DB --overwrite]

0.86

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-min 8 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --filter-mac-max 12 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-min 8 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-info DB --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-flag s50 --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-info H2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-distance 500 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-min 8 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --overwrite]

0.10

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-max 12 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 69.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-info H2 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --filter-distance 500 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-max 12 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --overwrite]

0.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --filter-mac-min 8 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-info DB --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-min 0.2 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-flag q10 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --filter-mac-max 12 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-distance 500 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-distance 500 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --filter-distance 500 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 69.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 69.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-info H2 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-include-info DB --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-flag q10 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-max 0.3 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-maf-max 0.3 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-maf-min 0.2 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-mac-min 8 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-include-info DB --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-include-info DB --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-flag s50 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-min 8 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-to-bp 2000000 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.6 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-flag s50 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-mac-max 12 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-maf-max 0.3 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-max 12 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-info DB --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-distance 500 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-include-info DB --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-info DB --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-min 8 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-info H2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-distance 500 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-info H2 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-min 8 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.89

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-max 12 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.83

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.83

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-min 0.2 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-min 0.2 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-from-bp 1000000 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-max 12 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-distance 500 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 480.0 kB CPU Usage: 79.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.5 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-distance 500 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-max 0.3 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-flag s50 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.9 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-distance 500 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-max 0.3 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-flag s50 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-flag q10 --filter-distance 500 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-from-bp 1000000 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.6 %

Passed

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-min 8 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-info DB --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.5 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-info DB --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-min 8 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 476.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-min 0.2 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-flag s50 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-max 12 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-flag s50 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-min 8 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-max 12 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-info DB --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-info H2 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-max 12 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-info H2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-min 8 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-distance 500 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-info DB --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-flag s50 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-info H2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-distance 500 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-min 0.2 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-distance 500 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-max 12 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-info DB --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-info H2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-min 0.2 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-distance 500 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-maf-max 0.3 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-info H2 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-flag s50 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-min 0.2 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-max 0.3 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --filter-include-info DB --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --filter-exclude-info H2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-mac-min 8 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-info DB --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-mac-max 12 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-max 0.3 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-min 8 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-min 0.2 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-max 0.3 --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-min 8 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 69.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-info H2 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-include-info DB --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-max 12 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-min 8 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-max 0.3 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-min 8 --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-max 12 --overwrite]

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-flag s50 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-min 0.2 --overwrite]

0.86

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-min 8 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-max 12 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.87

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.95

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

1.11

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

1.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

1.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

1.05

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-max 12 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

1.11

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

1.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

1.04

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.87

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

1.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-info DB --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

1.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.87

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.94

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

1.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

1.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.89

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-exclude-flag s50 --overwrite]

1.03

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-max 0.3 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

1.02

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-exclude-flag s50 --overwrite]

1.04

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --overwrite]

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

1.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-distance 500 --overwrite]

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-max 12 --overwrite]

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-distance 500 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-info H2 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-distance 500 --overwrite]

0.93

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-to-bp 2000000 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-flag s50 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-include-info DB --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-min 0.2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-include-info DB --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-min 8 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-distance 500 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-info DB --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-max 0.3 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 99.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-max 12 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --filter-include-info DB --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 79.7 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-min 8 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-distance 500 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-info H2 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-to-bp 2000000 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-max 12 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-min 0.2 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-flag s50 --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.93

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.93

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.93

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.83

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-max 0.3 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-distance 500 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.9 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --filter-include-info DB --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-min 8 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-info DB --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-max 12 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --filter-exclude-info H2 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-min 8 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-passed --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-info H2 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --filter-distance 500 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-info H2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-distance 500 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-distance 500 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-max 12 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.83

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-max 12 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-distance 500 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-min 0.2 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-min 0.2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.5 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-min 8 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-flag s50 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-distance 500 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-distance 500 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-max 12 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-positions chr1_sites.sites --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-flag s50 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-max 0.3 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-max 12 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-max 0.3 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-info DB --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-distance 500 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 536.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.10

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-min 8 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-min 8 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-distance 500 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-info DB --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --filter-mac-min 8 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-info DB --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-min 8 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-passed --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.6 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-min 8 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-max 12 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.7 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 99.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.7 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 88.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 460.0 kB CPU Usage: 79.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-info H2 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-max 12 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-info H2 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-distance 500 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-max 12 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --filter-mac-max 12 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --overwrite]

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.7 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-distance 500 --overwrite]

0.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-distance 500 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-min 0.2 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-distance 500 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-min 0.2 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --filter-distance 500 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-max 0.3 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 744.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-include-info DB --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-distance 500 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-min 8 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-max 0.3 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-flag q10 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 79.9 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-distance 500 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-include-info DB --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --filter-mac-max 12 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.71

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-min 8 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-max 12 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-passed --filter-distance 500 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-min 8 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 79.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-distance 500 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-flag q10 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --filter-include-info DB --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 480.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-exclude-info H2 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 88.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 79.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.1 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-include-info DB --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-max 12 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 88.2 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.6 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 99.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 99.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-distance 500 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.5 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-info H2 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-distance 500 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-flag q10 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 69.9 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 480.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-flag s50 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-flag q10 --filter-distance 500 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.2 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.6 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 78.7 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-info DB --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.4 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.9 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 136.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-passed --filter-include-info DB --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-flag s50 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-min 8 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 65.7 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-flag s50 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-info H2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-passed --filter-exclude-info H2 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-info DB --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-info DB --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-min 0.2 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-max 12 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-flag s50 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-max 0.3 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-info H2 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-passed --filter-include-info DB --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-min 0.2 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-min 8 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-min 0.2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-info DB --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 29.9 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 0.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 0.0 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-distance 500 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 10.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-flag q10 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 29.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 0.0 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-max 12 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 9.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 10.0 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 0.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 0.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-max 12 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 0.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 0.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 20.0 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 0.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-max 0.3 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-flag s50 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 0.0 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-mac-min 8 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 69.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.7 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.70

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 0.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-flag s50 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-min 0.2 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-min 8 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-flag s50 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-min 8 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-info DB --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 224.0 kB CPU Usage: 79.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-info DB --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 99.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-info DB --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 77.7 %

Passed

0.94

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.86

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.7 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-max 0.3 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-min 8 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.89

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

1.03

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

1.03

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-info H2 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-min 8 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Passed

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-min 0.2 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-min 8 --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.9 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-max 12 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-info H2 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-max 0.3 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --filter-exclude-flag s50 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-maf-max 0.3 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 224.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-to-bp 2000000 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-mac-min 8 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.8 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --filter-exclude-info H2 --overwrite]

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.2 %

Passed

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.3 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-min 0.2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.2 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.1 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.3 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 98.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.5 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.2 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 480.0 kB CPU Usage: 99.0 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-max 12 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 98.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.4 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.3 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-max 0.3 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 98.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-mac-max 12 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 99.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 88.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 87.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-max 12 --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.12

----------------------------- Captured stdout call -----------------------------
Memory Usage: 464.0 kB CPU Usage: 89.7 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-distance 500 --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.6 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 85.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 98.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.0 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.5 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 95.1 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.1 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.1 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 88.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 88.8 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Passed

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1216.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 93.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3360.0 kB CPU Usage: 99.3 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 91.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-min 8 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1216.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 84.2 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 92.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.5 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.6 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 86.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 78.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 136.0 kB CPU Usage: 97.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 79.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1212.0 kB CPU Usage: 89.6 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 95.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.2 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 69.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 808.0 kB CPU Usage: 99.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1720.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-from-bp 1000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 92.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.3 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 96.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1464.0 kB CPU Usage: 94.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.1 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 88.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 98.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 79.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.2 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-positions chr1_sites.sites --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2568.0 kB CPU Usage: 99.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 200.0 kB CPU Usage: 94.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.0 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 86.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1216.0 kB CPU Usage: 89.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 99.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3624.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.3 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 88.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2568.0 kB CPU Usage: 92.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 98.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.7 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 90.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 476.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 98.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.1 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.7 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-maf-max 0.3 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-distance 500 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.1 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1196.0 kB CPU Usage: 89.6 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.7 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.7 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.4 %

Passed

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1968.0 kB CPU Usage: 99.1 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2228.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1072.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-passed --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 99.6 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-maf-min 0.2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.4 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-flag s50 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --overwrite]

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 180.0 kB CPU Usage: 99.3 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 93.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 88.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1720.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 95.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.0 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.5 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.1 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 94.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 95.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 90.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-flag q10 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 176.0 kB CPU Usage: 99.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 87.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-maf-max 0.3 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 99.1 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 86.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-from-bp 1000000 --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 98.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 804.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 78.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 94.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-info DB --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 96.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.7 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.4 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 95.1 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.2 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 90.9 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.0 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 88.6 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 94.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 96.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 95.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 85.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 97.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-positions chr1_sites.sites --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 85.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2832.0 kB CPU Usage: 98.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.1 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 98.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 948.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 92.3 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.7 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 88.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 87.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.3 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.5 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.1 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.2 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 79.7 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 948.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3360.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 97.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 98.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 79.5 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1068.0 kB CPU Usage: 89.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 88.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 94.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 98.5 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 95.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.3 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 95.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 92.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 86.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 97.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 95.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.2 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 83.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1964.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 95.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 79.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-bed chr1_sites.bed --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.4 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 91.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 808.0 kB CPU Usage: 99.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 88.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-positions chr1_sites.sites --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 92.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.6 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 97.3 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.9 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-max 0.3 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-distance 500 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1212.0 kB CPU Usage: 89.7 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 86.1 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 4096.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-exclude-flag s50 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 91.4 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-from-bp 1000000 --filter-include-info DB --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 93.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 87.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.0 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-min 8 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-flag s50 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.6 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 256.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 92.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-flag q10 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 90.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 548.0 kB CPU Usage: 99.0 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 91.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-mac-max 12 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 96.4 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.5 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-mac-max 12 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-bed chr1_sites.bed --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 79.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-positions chr1_sites.sites --filter-include-info DB --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 94.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 88.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-exclude-flag s50 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 2832.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 93.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 96.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-distance 500 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1464.0 kB CPU Usage: 96.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 95.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 95.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 99.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 92.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-flag s50 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3624.0 kB CPU Usage: 93.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.0 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 98.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 81.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 95.9 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 85.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-distance 500 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 95.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.6 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 74.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 268.0 kB CPU Usage: 89.0 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-info H2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-bed chr1_sites.bed --filter-include-info DB --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.3 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 88.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 4100.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-flag q10 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 98.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-passed --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 91.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 93.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 98.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 86.5 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 93.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-positions chr1_sites.sites --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.1 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-bed chr1_sites.bed --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-bed chr1_sites.bed --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-positions chr1_sites.sites --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 88.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-to-bp 2000000 --filter-distance 500 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.2 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 86.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-positions chr1_sites.sites --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 93.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 93.2 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 97.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-mac-min 8 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 98.9 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 98.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-maf-max 0.3 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 88.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.1 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 98.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 98.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.6 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-from-bp 1000000 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3624.0 kB CPU Usage: 95.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-to-bp 2000000 --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 88.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-flag q10 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.4 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-info H2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 91.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1196.0 kB CPU Usage: 79.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1964.0 kB CPU Usage: 97.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 98.5 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-passed --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.2 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 88.0 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 97.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-from-bp 1000000 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.2 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-to-bp 2000000 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.1 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.6 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 86.9 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 86.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.4 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-min-alleles 2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 99.5 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.2 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1212.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-maf-min 0.2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 3624.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-chr chr1 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 98.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-chr chr2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.7 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.6 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 97.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-flag s50 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-missing 1.0 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 98.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-chr chr2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 93.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-max-missing 1.0 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-alleles 4 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-exclude-flag s50 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-positions chr1_sites.sites --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 812.0 kB CPU Usage: 89.3 %

Passed

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.6 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.2 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 89.0 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-chr chr1 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-chr chr1 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-to-bp 2000000 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-chr chr2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-min-alleles 2 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-mac-max 12 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 95.6 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-missing 1.0 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-chr chr1 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-max-alleles 4 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-maf-max 0.3 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.4 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 88.7 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 99.5 %

Passed

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-min-alleles 2 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 98.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 95.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-missing 1.0 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 92.9 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.5 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 87.4 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-chr chr2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-max-missing 1.0 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-include-chr chr1 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-min-alleles 2 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-min 8 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-chr chr1 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-chr chr2 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.7 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-bed chr1_sites.bed --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-max-missing 1.0 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-alleles 4 --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-chr chr2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-min-alleles 2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-min-alleles 2 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-max-alleles 4 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-alleles 4 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-chr chr2 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-exclude-chr chr2 --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-min 8 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-min-alleles 2 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-flag q10 --filter-mac-min 8 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-chr chr2 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-alleles 4 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-chr chr1 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-alleles 4 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-alleles 4 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-alleles 4 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-chr chr2 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-exclude-bed chr1_sites.bed --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-max-missing 1.0 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-alleles 4 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-chr chr1 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-alleles 4 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-chr chr2 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-chr chr2 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-chr chr2 --filter-include-passed --filter-mac-max 12 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-chr chr1 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-chr chr1 --filter-include-passed --filter-mac-max 12 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.11

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-chr chr2 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-chr chr2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.11

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-chr chr2 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-missing 1.0 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-missing 1.0 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 89.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-chr chr1 --overwrite]

0.11

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-chr chr1 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-missing 1.0 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-chr chr1 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-max-missing 1.0 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-min-alleles 2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-missing 1.0 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-chr chr1 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-max-alleles 4 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-chr chr2 --overwrite]

0.93

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-exclude-chr chr2 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-missing 1.0 --overwrite]

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-max-alleles 4 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-min-alleles 2 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-max-alleles 4 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-chr chr1 --overwrite]

0.69

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-max-alleles 4 --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-chr chr2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-chr chr2 --overwrite]

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-chr chr2 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-alleles 4 --overwrite]

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-missing 1.0 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-missing 1.0 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-missing 1.0 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-exclude-chr chr2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-min-alleles 2 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-chr chr1 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-max-missing 1.0 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-chr chr1 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-chr chr1 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.9 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-chr chr1 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-max-missing 1.0 --overwrite]

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

0.85

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-flag q10 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-chr chr1 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-chr chr2 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-max-missing 1.0 --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-max-alleles 4 --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 79.8 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-min-alleles 2 --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-chr chr2 --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-chr chr1 --overwrite]

0.89

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

0.94

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-max-missing 1.0 --overwrite]

0.84

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-max-alleles 4 --overwrite]

0.76

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-bed chr1_sites.bed --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.60

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-chr chr2 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-chr chr1 --overwrite]

0.94

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-chr chr2 --overwrite]

0.95

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-missing 1.0 --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-chr chr1 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-chr chr1 --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv Pan_paniscus-9731_LB502 --filter-max-missing 1.0 --overwrite]

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-min-alleles 2 --overwrite]

0.79

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-bed chr1_sites.bed --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-chr chr1 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-positions chr1_sites.sites --overwrite]

0.50

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-min-alleles 2 --overwrite]

0.11

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-bed chr1_sites.bed --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-max-alleles 4 --overwrite]

0.91

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-passed --overwrite]

0.81

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-min-alleles 2 --overwrite]

0.94

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-passed --overwrite]

0.82

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-bed chr1_sites.bed --overwrite]

0.65

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-bed chr1_sites.bed --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-positions chr1_sites.sites --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-passed --overwrite]

0.51

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-passed --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 79.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-indv-file Paniscus.txt --filter-include-chr chr1 --overwrite]

1.04

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-flag q10 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-max-missing 1.0 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-passed --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-positions chr1_sites.sites --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-chr chr2 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-passed --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-bed chr1_sites.bed --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-passed --filter-include-flag q10 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-chr chr1 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-positions chr1_sites.sites --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-passed --filter-include-flag q10 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-include-chr chr1 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-bed chr1_sites.bed --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-passed --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-passed --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-positions chr1_sites.sites --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-exclude-chr chr2 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-bed chr1_sites.bed --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-min-alleles 2 --filter-include-chr chr1 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-chr chr2 --overwrite]

0.57

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-indv Pan_paniscus-A914_Hortense --filter-include-chr chr1 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-passed --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-positions chr1_sites.sites --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-max-alleles 4 --filter-include-chr chr1 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-alleles 4 --filter-max-missing 1.0 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-positions chr1_sites.sites --overwrite]

0.80

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-min-alleles 2 --filter-exclude-chr chr2 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-flag q10 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-to-bp 2000000 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-passed --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-max-missing 1.0 --filter-exclude-chr chr2 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-passed --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-flag q10 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-passed --filter-include-flag q10 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-bed chr1_sites.bed --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-passed --overwrite]

0.73

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-passed --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-exclude-bed chr1_sites.bed --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-flag q10 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-bed chr1_sites.bed --overwrite]

0.75

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-flag q10 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-to-bp 2000000 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.16

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-passed --filter-include-flag q10 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-flag q10 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-bed chr1_sites.bed --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-bed chr1_sites.bed --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-passed --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.91

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.72

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-flag q10 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-passed --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-flag q10 --overwrite]

0.96

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-to-bp 2000000 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-to-bp 2000000 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-to-bp 2000000 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-flag q10 --overwrite]

0.97

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-bed chr1_sites.bed --overwrite]

0.77

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-flag q10 --overwrite]

0.88

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.78

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-flag q10 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-passed --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-positions chr1_sites.sites --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-passed --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-passed --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-bed chr1_sites.bed --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-positions chr1_sites.sites --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-flag q10 --overwrite]

0.56

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-passed --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.74

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-passed --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-to-bp 2000000 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-flag q10 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-positions chr1_sites.sites --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-bed chr1_sites.bed --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 79.8 %

Passed

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-passed --filter-include-flag q10 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-passed --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-passed --overwrite]

0.67

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-flag q10 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-passed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-flag q10 --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.8 %

Passed

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-passed --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-to-bp 2000000 --overwrite]

0.13

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 99.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-flag q10 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 99.7 %

Passed

0.14

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-positions chr1_sites.sites --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-passed --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-passed --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-passed --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 98.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-passed --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-flag q10 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-positions chr1_sites.sites --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-passed --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-passed --overwrite]

0.24

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-passed --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-to-bp 2000000 --filter-include-passed --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-info DB --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-info DB --filter-maf-min 0.2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-passed --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 99.8 %

Passed

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-passed --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-info DB --filter-mac-max 12 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-exclude-bed chr1_sites.bed --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-include-bed chr1_sites.bed --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 99.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-passed --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-positions chr1_sites.sites --filter-include-flag q10 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-min 8 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-info DB --filter-maf-max 0.3 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-passed --overwrite]

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-max 0.3 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-from-bp 1000000 --filter-exclude-bed chr1_sites.bed --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 89.8 %

Passed

0.31

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-bed chr1_sites.bed --filter-include-passed --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-positions chr1_sites.sites --filter-include-passed --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-passed --filter-include-flag q10 --overwrite]

0.30

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-include-info DB --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-max 0.3 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-info DB --filter-mac-min 8 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-min 0.2 --overwrite]

0.38

----------------------------- Captured stdout call -----------------------------
Memory Usage: 956.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-min 8 --overwrite]

0.39

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-distance 500 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-max 12 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-exclude-info H2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-include-info DB --filter-exclude-info H2 --overwrite]

0.45

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-max 12 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-distance 500 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-min 0.2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-exclude-info H2 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-bed chr1_sites.bed --filter-include-flag q10 --overwrite]

0.15

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-info DB --filter-maf-max 0.3 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-max 12 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-min 8 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-maf-max 0.3 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-min 8 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-distance 500 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-max 12 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-min 8 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-include-info DB --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-mac-min 8 --filter-distance 500 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-mac-min 8 --filter-distance 500 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-max 12 --overwrite]

0.42

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-include-info DB --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-min 8 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-distance 500 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-max 0.3 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-min 8 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-mac-min 8 --filter-mac-max 12 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf --out-prefix chr11_vcf --filter-mac-max 12 --filter-distance 500 --overwrite]

0.33

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-min 0.2 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-min 8 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-distance 500 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-min 0.2 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-max 12 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-exclude-info H2 --overwrite]

0.34

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-max 0.3 --overwrite]

0.49

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-distance 500 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-min 8 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-info DB --filter-maf-max 0.3 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-info DB --filter-mac-min 8 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-info DB --filter-maf-min 0.2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-min 0.2 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-min 8 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-max 12 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-maf-max 0.3 --overwrite]

0.29

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-info DB --filter-mac-max 12 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-info DB --filter-exclude-info H2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-min 8 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-info DB --filter-distance 500 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-info DB --filter-mac-max 12 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-max 0.3 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-min 8 --overwrite]

0.43

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-max 12 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-info DB --filter-mac-min 8 --overwrite]

0.44

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-max 12 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-info DB --filter-mac-min 8 --overwrite]

0.62

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-mac-min 8 --filter-mac-max 12 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 216.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-max 12 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-info H2 --filter-distance 500 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-info DB --filter-exclude-info H2 --overwrite]

0.61

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-include-info DB --filter-maf-min 0.2 --overwrite]

0.52

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-info DB --filter-maf-min 0.2 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-info DB --filter-maf-max 0.3 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-max 0.3 --overwrite]

0.26

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-maf-max 0.3 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-distance 500 --overwrite]

0.48

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-max 0.3 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-min 8 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 212.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-exclude-info H2 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-min 8 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-min 0.2 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-min 8 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-mac-min 8 --filter-mac-max 12 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-mac-max 12 --filter-distance 500 --overwrite]

0.58

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-info DB --filter-distance 500 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format vcf.gz --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-distance 500 --overwrite]

0.68

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-distance 500 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-distance 500 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-info DB --filter-distance 500 --overwrite]

0.59

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-min 0.2 --overwrite]

0.53

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-exclude-info H2 --overwrite]

0.32

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-include-info DB --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-exclude-info H2 --overwrite]

0.40

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-distance 500 --overwrite]

0.47

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 89.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-max 12 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-include-info DB --filter-exclude-info H2 --overwrite]

0.66

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-info DB --filter-maf-min 0.2 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-distance 500 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-maf-max 0.3 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-min 8 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-min 8 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-mac-min 8 --filter-distance 500 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-max 12 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-include-info DB --filter-mac-max 12 --overwrite]

0.41

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-distance 500 --overwrite]

0.54

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-mac-min 8 --filter-distance 500 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-info DB --filter-mac-min 8 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-max 0.3 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-distance 500 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-info DB --filter-mac-max 12 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-info DB --filter-distance 500 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-max 0.3 --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-mac-max 12 --filter-distance 500 --overwrite]

0.63

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-distance 500 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-max 12 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-mac-min 8 --filter-mac-max 12 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-include-info DB --overwrite]

0.35

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-mac-max 12 --filter-distance 500 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 484.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-distance 500 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-distance 500 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-min 0.2 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-info DB --filter-maf-max 0.3 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-max 12 --overwrite]

0.64

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-min 8 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-info DB --filter-exclude-info H2 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-maf-max 0.3 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-min 0.2 --overwrite]

0.36

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format bcf --out-prefix chr11_vcf --filter-mac-min 8 --filter-mac-max 12 --overwrite]

0.55

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-min 8 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-info DB --filter-mac-max 12 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 228.0 kB CPU Usage: 69.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-mac-max 12 --overwrite]

0.46

----------------------------- Captured stdout call -----------------------------
Memory Usage: 488.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-max 12 --overwrite]

0.37

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 69.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-distance 500 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-mac-max 12 --overwrite]

0.28

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-max 12 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 140.0 kB CPU Usage: 88.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-distance 500 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-distance 500 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 88.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-mac-min 8 --filter-distance 500 --overwrite]

0.17

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 101.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-distance 500 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-min 0.2 --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 92.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-include-info DB --overwrite]

0.18

----------------------------- Captured stdout call -----------------------------
Memory Usage: 8.0 kB CPU Usage: 99.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 85.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-max 0.3 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 86.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-max 12 --overwrite]

0.19

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 96.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-max 0.3 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 764.0 kB CPU Usage: 92.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-mac-max 12 --filter-distance 500 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 92.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-info DB --filter-exclude-info H2 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 760.0 kB CPU Usage: 85.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-include-info DB --filter-maf-max 0.3 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 91.7 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-distance 500 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 204.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-mac-min 8 --filter-mac-max 12 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 89.6 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-mac-max 12 --filter-distance 500 --overwrite]

0.20

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-max 0.3 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.4 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-maf-min 0.2 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 90.2 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-info DB --filter-distance 500 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 99.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-distance 500 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 500.0 kB CPU Usage: 89.1 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-info DB --filter-mac-min 8 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 79.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-include-info DB --filter-exclude-info H2 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 92.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-exclude-info H2 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1208.0 kB CPU Usage: 87.0 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-include-info DB --filter-maf-min 0.2 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 952.0 kB CPU Usage: 86.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-mac-max 12 --filter-distance 500 --overwrite]

0.21

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 98.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-maf-min 0.2 --filter-mac-max 12 --overwrite]

0.22

----------------------------- Captured stdout call -----------------------------
Memory Usage: 144.0 kB CPU Usage: 89.3 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-distance 500 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 232.0 kB CPU Usage: 79.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_sites --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-max 12 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 504.0 kB CPU Usage: 89.5 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-flag s50 --filter-maf-max 0.3 --overwrite]

0.23

----------------------------- Captured stdout call -----------------------------
Memory Usage: 960.0 kB CPU Usage: 91.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format removed_bed --out-prefix chr11_vcf --filter-exclude-info H2 --filter-mac-min 8 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 46.8 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_sites --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-distance 500 --overwrite]

0.25

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1204.0 kB CPU Usage: 49.9 %

Passed

test_1.py::test_filter[python vcf_filter.py --vcf chr11.unfiltered.vcf --out-format kept_bed --out-prefix chr11_vcf --filter-maf-max 0.3 --filter-distance 500 --overwrite]

0.27

----------------------------- Captured stdout call -----------------------------
Memory Usage: 1200.0 kB CPU Usage: 39.9 %

vcf_filter_test_suite.html

Environment

Summary

Results